Teenage hosts Araya and Christina investigate paranormal or global historical reports of mysteries such as legendary creatures/monsters, disembodied spirits, dinosaurs and aliens/unidentified flying objects.
Next comes the "Mystery Lab" segment featuring Doubting Dave doing some kind of experiment or laboratory demonstration to illustrate a point that is most often related to that week's theme.
At the conclusion of each program, the hosts appear together in a comedic wrap-up link, usually closing out with the Mystery Hunters signature tag-line: "Remember, things aren't always what they seem!"
Another DVD was released early December 2007, titled Mystery Hunters: Alien Encounters, featuring three episodes from the series about the said topic.
The website was produced in an 'interactive comic book' format containing 13 episodic adventures featuring intro and closing videos from Christina and Araya, quizzes in Doubting Dave's voice, and puzzle games and animation following themes presented in the show.